Sequence
atgc intronic sequence ATGC exonic sequencegtaagttagctactaacccgcctaatgtcatatttggatcagatctctctgttttaattgcaataaccaagccacattctcttactccctggggtgtttcagAATGCAAGCACAGGGGAGAATGAAACACTTCTTGCTGTTGGGACTGCGTATGTCCAAGGGGAGGATGTTGCTGCAAGGGGCCGTGTGCTTCTTTTCTCTT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G51660.1 |
intron # | 21 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G51660.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: LOC_Os04g18010.1 (Oryza sativa), 3'ss of exon 21
----gtaagttagct-actaacccgcctaatgtcatatttggatcagatctctct-gttttaattgcaataaccaagccacattctcttactccctggggtgtttcagAATGCAAGCACAGGGGAGAATGAAACACTTCTTGCTGTTGGGACTGCGTATGTCCAAGGGGAGGATGTTGCTGCAAGGGGCCGTGTGCTTCTTTTCTCTT
| | ||| || | ||||| || || || || ||| | | ||||||| | || || ||| | | | | |||||||| ||| ||| ||| ||||| || || | || |||||||||| ||||| | ||||||||||| ||||| || || ||||||||||| |||||||
gcttgagatttatcttgtttgaaaatttaatg--atcaaaggtacacatgtctgtaggtttaattatattattcactgaacagttatgcatttt------tacttcagAATACAACCACCAAGGAAAATGAGACCCTGTTGGCCATTGGGACTGCTTATGTTCTTGGGGAGGATGTAGCTGCTAGAGGACGTGTGCTTCTGTTCTCTT
upper sequence: AT5G51660.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GRMZM2G453879_T02 (Zea mays), 3'ss of exon 6
gtaagttagctactaacccgcctaatgtcatatttggatcagatctctctgttttaattgcaataaccaagccacattctcttactccctggggtgtttcagAATGCAAGCACAGGGGAGAATGAAACACTTCTTGCTGTTGGGACTGCGTATGTCCAAGGGGAGGATGTTGCTGCAAGGGGCCGTGTGCTTCTTTTCTCTT
| || | ||| | ||| |||| | |||| | | |||| | ||| | | | | | | |||||| || || ||| |||||||| || | || |||| ||||| ||||| |||||||||||||||||||| || || || |||||||| |||||||
--------gtatgtatgtcttctacacttgtat--ggatactgcactcaaactaaaattttatttaccaga--atattat-tgattttc------gcctcagAACACATCTACGAAGGAAAATGAAACCCTGATGGCCATTGGAACTGCTTATGTTCAAGGGGAGGATGTTGCTGCTAGAGGACGGGTGCTTCTGTTCTCTT
upper sequence: AT5G51660.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GRMZM2G453879_T01 (Zea mays), 3'ss of exon 6
gtaagttagctactaacccgcctaatgtcatatttggatcagatctctctgttttaattgcaataaccaagccacattctcttactccctggggtgtttcagAATGCAAGCACAGGGGAGAATGAAACACTTCTTGCTGTTGGGACTGCGTATGTCCAAGGGGAGGATGTTGCTGCAAGGGGCCGTGTGCTTCTTTTCTCTT
| || | ||| | ||| |||| | |||| | | |||| | ||| | | | | | | |||||| || || ||| |||||||| || | || |||| ||||| ||||| |||||||||||||||||||| ||
--------gtatgtatgtcttctacacttgtat--ggatactgcactcaaactaaaattttatttaccagA--ATATTAT-TGATTTTC------GCCTCAGAACACATCTACGAAGGAAAATGAAACCCTGATGGCCATTGGAACTGCTTATGTTCAAGGGGAGGATGTTGCTGCTAG-----------------------
upper sequence: AT5G51660.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GLYMA09G28030.1 (Glycine max), 3'ss of exon 21
gtaagttagctactaacccgcctaatgtcatatttggatcagatctctctgttttaattgc-aataaccaagccacattctcttactccctggggtgttt----cagAATGCAAGCACAGGGGAGAATGAAACACTTCTTGCTGTTGGGACTGCGTATGTCCAAGGGGAGGATGTTGCTGCAAGGGGCCGTGTGCTTCTTTTCTCTT
| | ||| | | | | | || | ||| || | || | | | | | | | ||| |||||| ||| | || || |||||||||||| | || |||| ||||| ||||| ||||| ||||||||||||||||| || ||| | || | |||||||
------------------------gtaatgttttttgctttggcttttgaattgtggatgctgattatt--gctgaaccttataaatgaaaatgatctttattgcagAATACAACCTCAAAAGAAAATGAAACACTTTTAGCCATTGGTACTGCTTATGTGCAAGGAGAGGATGTTGCTGCAAGAGGACGTATCCTCTTGTTCTCTT
upper sequence: AT5G51660.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GLYMA16G32890.1 (Glycine max), 3'ss of exon 21
gtaagttagctactaacccgcctaatgtcatatttggatcagatctctctgttttaattgcaataaccaagccacattctcttactccctggggtgtttcagAATGCAAGCACAGGGGAGAATGAAACACTTCTTGCTGTTGGGACTGCGTATGTCCAAGGGGAGGATGTTGCTGCAAGGGGCCGTGTGCTTCTTTTCTCTT
||| | | || | || | ||| || |||| |||| | ||||| | | || |||||| ||| | || || |||||||||||| | || |||| ||||| ||||| ||||| ||||||||||||||||| || ||| | || | |||||||
------------gtaatgtttgttcctttggtttacaaattgaggttgctgatt--gttgctg-aaccttataaatttctcagaaatttatctttattgcagAATACAACCTCAAAAGAAAATGAAACACTTTTAGCCATTGGTACTGCTTATGTGCAAGGAGAGGATGTTGCTGCAAGAGGACGTATCCTATTGTTCTCTT
upper sequence: AT5G51660.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: Vv16s0022g01860.t01 (Vitis vinifera), 3'ss of exon 21
---------------------------------------------------------------------------------------------gtaagttagctactaacccgcctaatgtcatatttggatcag-atctctctg-ttttaattgcaa--taaccaagccacattctcttactccctggggtgttt-cagAATGCAAGCACAGGGGAGAATGAAACACTTCTTGCTGTTGGGACTGCGTATGTCCAAGGGGAGGATGTTGCTGCAAGGGGCCGTGTGCTTCTTTTCTCTT
|| | | | || | || | ||| | | | | | | || | ||| | | | || | |||| || | | |||||| | | |||| || |||||||||||| | || |||||||||| || || |||||||||||||||||||||||||| || |||||| | || |||
gtgagttaattctttgccattccaactgtttctttgtgttttggttttggcttctttcttgaattctcgtcatgggagaggcgtgtggtgagtgttggggggggattagatatgttcttggtgaagctgggttggtgtttgtttaattcttatttctgcctgttctagaaaatcataattaccatgtgtcttacctgcagAATACTACCACAAAAGAAAATGAAACACTTTTGGCCATTGGGACTGCTTACGTACAAGGGGAGGATGTTGCTGCAAGGGGACGGGTGCTTTTATTTTCTG
upper sequence: AT5G51660.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: PP1S61_42V6.1 (Physcomitrella patens), 3'ss of exon 23
gtaagttagctactaacccgcctaatgtcatatttggatcagatctctctgttttaattgcaataaccaagccacattctcttactc----cctggggtgtttcagAATGCAAGCACAGGGGAGAATGAAACACTTCTTGCTGTTGGGACTGCGTATGTCCAAGGGGAGGATGTTGCTGCAAGGGGCCGTGTGCTTCTTTTCTCTT
|| || || | | |||| | | || || || |||| |||| || | | || | ||||| | |||| ||| ||||| | |||| ||| | || | |||||| |||| || ||||||| |||||||||||||||||||||| || || | | ||| |||||
---gatt--ctttcaagctccataatttttgaggtgc-tctaattgaggcgtttgaattaatatcaatcatttgcagtgtcttattaattgtttgggatgtcgcagAACATCACAACAGATCAGACACAGACCTTACTTGCTATTGGTACATCGTATGTACAAGGGGAGGATGTTGCTGCAAAAGGTCGGATTATACTTGTCTCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctgttttaattgcaataaccaagccacattctcttactccctggggtgtttcagAATGCAAGCACAGGGGAGAATGAAACACTTCTTGCTGTTGGGACTGCGTATGTCCAAGGGGAGGATGTTGCTGCAAGGGGCCGTGTGCTTCTTTTCTCTT
tttaattgcaataa TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttagctactaacccgcctaatgtcatatttggatcagatctctctgttttaattgcaataaccaagccacattctcttactccctggggtgtttcagAATGCAAGCACAGGGGAGAATGAAACACTTCTTGCTGTTGGGACTGCGTATGTCCAAGGGGAGGATGTTGCTGCAAGGGGCCGTGTGCTTCTTTTCTCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC